Published in Cold Spring Harb Protoc on January 01, 2010
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Complete nitrification by a single microorganism. Nature (2015) 1.72
Antibiotics in feed induce prophages in swine fecal microbiomes. MBio (2011) 1.72
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A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). PLoS One (2012) 1.44
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Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS One (2014) 1.37
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. J Allergy Clin Immunol (2012) 1.35
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A Canadian Working Group report on fecal microbial therapy: microbial ecosystems therapeutics. Can J Gastroenterol (2012) 1.25
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Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection. PLoS One (2012) 1.23
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput Biol (2016) 1.22
Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci (2014) 1.15
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Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules. Curr Opin Microbiol (2010) 1.12
Analysis of 16S rRNA environmental sequences using MEGAN. BMC Genomics (2011) 1.03
Human and environmental impacts on river sediment microbial communities. PLoS One (2014) 1.03
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. Brief Bioinform (2012) 1.02
Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. Elife (2014) 1.01
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The preterm placental microbiome varies in association with excess maternal gestational weight gain. Am J Obstet Gynecol (2014) 0.98
Analytical tools and databases for metagenomics in the next-generation sequencing era. Genomics Inform (2013) 0.98
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The placental membrane microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis. Am J Obstet Gynecol (2016) 0.95
Diet shapes the gut microbiome of pigs during nursing and weaning. Microbiome (2015) 0.94
Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization. PLoS One (2014) 0.93
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Convergent bacterial microbiotas in the fungal agricultural systems of insects. MBio (2014) 0.90
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Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations. MBio (2014) 0.86
Estimation of viral richness from shotgun metagenomes using a frequency count approach. Microbiome (2013) 0.85
Polyphasic analysis of a middle ages coprolite microbiota, Belgium. PLoS One (2014) 0.84
Metagenomics, paratransgenesis and the Anopheles microbiome: a portrait of the geographical distribution of the anopheline microbiota based on a meta-analysis of reported taxa. Mem Inst Oswaldo Cruz (2014) 0.84
Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. Brief Bioinform (2015) 0.83
Seasonally variable intestinal metagenomes of the red palm weevil (Rhynchophorus ferrugineus). Environ Microbiol (2013) 0.83
MOCAT2: a metagenomic assembly, annotation and profiling framework. Bioinformatics (2016) 0.82
Analysis of the First Temperate Broad Host Range Brucellaphage (BiPBO1) Isolated from B. inopinata. Front Microbiol (2016) 0.82
Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist's Perspective - Not Only Size Matters! PLoS One (2017) 0.82
Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci Rep (2015) 0.82
MetaMicrobesOnline: phylogenomic analysis of microbial communities. Nucleic Acids Res (2012) 0.81
Metatranscriptomic evidence for co-occurring top-down and bottom-up controls on toxic cyanobacterial communities. Appl Environ Microbiol (2015) 0.81
Complete Nucleotide Sequence of pVv01, a P1-Like Plasmid Prophage of Vibrio vulnificus. Genome Announc (2014) 0.81
Elviz - exploration of metagenome assemblies with an interactive visualization tool. BMC Bioinformatics (2015) 0.80
MetaBinG: using GPUs to accelerate metagenomic sequence classification. PLoS One (2011) 0.80
Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets. mSystems (2017) 0.79
The use of metagenomic approaches to analyze changes in microbial communities. Microbiol Insights (2013) 0.79
Functional Metagenomics of the Bronchial Microbiome in COPD. PLoS One (2015) 0.79
Gut microbiota Modulated by Probiotics and Garcinia cambogia Extract Correlate with Weight Gain and Adipocyte Sizes in High Fat-Fed Mice. Sci Rep (2016) 0.78
F1 and tbilisi are closely related brucellaphages exhibiting some distinct nucleotide variations which determine the host specificity. Genome Announc (2014) 0.78
The perinatal microbiome and pregnancy: moving beyond the vaginal microbiome. Cold Spring Harb Perspect Med (2015) 0.78
Microbial bioinformatics for food safety and production. Brief Bioinform (2015) 0.78
Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary. Front Microbiol (2016) 0.78
Environmental Breviatea harbour mutualistic Arcobacter epibionts. Nature (2016) 0.78
Microbial community analysis of pH 4 thermal springs in Yellowstone National Park. Extremophiles (2016) 0.78
Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. Sci Rep (2016) 0.77
Cannabis microbiome sequencing reveals several mycotoxic fungi native to dispensary grade Cannabis flowers. F1000Res (2015) 0.76
MLgsc: A Maximum-Likelihood General Sequence Classifier. PLoS One (2015) 0.76
MG-Digger: An Automated Pipeline to Search for Giant Virus-Related Sequences in Metagenomes. Front Microbiol (2016) 0.76
Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families. Sci Rep (2017) 0.75
Class prediction and feature selection with linear optimization for metagenomic count data. PLoS One (2013) 0.75
Characterization of saliva microbiota's functional feature based on metagenomic sequencing. Springerplus (2016) 0.75
Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research. Front Cell Infect Microbiol (2017) 0.75
Syntrophic linkage between predatory Carpediemonas and specific prokaryotic populations. ISME J (2017) 0.75
Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics. Front Microbiol (2017) 0.75
Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics. J Environ Eng (New York) (2016) 0.75
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. Database (Oxford) (2016) 0.75
Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden. PLoS One (2016) 0.75
Deep insights into carbohydrate metabolism in the rumen of Mehsani buffalo at different diet treatments. Genom Data (2015) 0.75
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. Front Genet (2017) 0.75
Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. Front Microbiol (2015) 0.75
Campylobacter group II phage CP21 is the prototype of a new subgroup revealing a distinct modular genome organization and host specificity. BMC Genomics (2015) 0.75
Metagenome phylogenetic profiling of microbial community evolution in a tetrachloroethene-contaminated aquifer responding to enhanced reductive dechlorination protocols. Stand Genomic Sci (2016) 0.75
Variable habitat conditions drive species covariation in the human microbiota. PLoS Comput Biol (2017) 0.75
HirBin: high-resolution identification of differentially abundant functions in metagenomes. BMC Genomics (2017) 0.75
Investigating a holobiont: Microbiota perturbations and transkingdom networks. Gut Microbes (2016) 0.75
MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets. PLoS One (2016) 0.75
Use of Metatranscriptomics in Microbiome Research. Bioinform Biol Insights (2016) 0.75
Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils. PLoS One (2017) 0.75
MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics. BMC Bioinformatics (2017) 0.75
Influence of Diet Composition on Cattle Rumen Methanogenesis: A Comparative Metagenomic Analysis in Indian and Exotic Cattle. Indian J Microbiol (2017) 0.75
Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars. Front Microbiol (2017) 0.75
The RAST Server: rapid annotations using subsystems technology. BMC Genomics (2008) 175.18
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res (2005) 29.61
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res (2006) 11.15
Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chem Rev (2007) 8.23
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. Stand Genomic Sci (2010) 6.30
Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci (2010) 4.70
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J Biotechnol (2003) 4.40
The Genomic Standards Consortium. PLoS Biol (2011) 3.99
A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science (2004) 3.87
Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ Microbiol (2006) 3.79
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience (2012) 3.24
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol (2005) 3.12
Gender bias in autoimmunity is influenced by microbiota. Immunity (2013) 2.88
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol (2006) 2.69
The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol (2009) 2.61
Finding novel genes in bacterial communities isolated from the environment. Bioinformatics (2006) 2.55
The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol (2006) 2.43
Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol (2007) 2.43
PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics (2002) 2.43
Metagenomics - a guide from sampling to data analysis. Microb Inform Exp (2012) 2.42
Complete genome sequence and analysis of Wolinella succinogenes. Proc Natl Acad Sci U S A (2003) 2.10
Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol (2012) 2.08
Development of joint application strategies for two microbial gene finders. Bioinformatics (2004) 2.00
The United States of America and scientific research. PLoS One (2010) 1.98
Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Appl Environ Microbiol (2007) 1.82
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora. J Bacteriol (2005) 1.77
BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics (2004) 1.73
Red death in Caenorhabditis elegans caused by Pseudomonas aeruginosa PAO1. Proc Natl Acad Sci U S A (2009) 1.69
Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J (2012) 1.66
EMMA: a platform for consistent storage and efficient analysis of microarray data. J Biotechnol (2003) 1.62
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics (2012) 1.61
Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. J Bacteriol (2006) 1.48
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics (2011) 1.48
Meeting Report: BioSharing at ISMB 2010. Stand Genomic Sci (2010) 1.47
Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants. Microbiome (2013) 1.43
Transcriptional changes in response to arbuscular mycorrhiza development in the model plant Medicago truncatula. Mol Plant Microbe Interact (2003) 1.36
Domain specificity in experimental measures and participant recruitment: an application to risk-taking behavior. Psychol Sci (2006) 1.36
The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics (2008) 1.34
Hybrid pathogenicity island PAGI-5 contributes to the highly virulent phenotype of a Pseudomonas aeruginosa isolate in mammals. J Bacteriol (2008) 1.33
Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. Appl Environ Microbiol (2006) 1.31
Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression. J Biotechnol (2003) 1.30
REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Appl Bioinformatics (2006) 1.27
The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. J Biotechnol (2009) 1.26
The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity. J Bacteriol (2008) 1.22
The future of microbial metagenomics (or is ignorance bliss?). ISME J (2010) 1.20
A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE. PLoS Comput Biol (2012) 1.18
Standard colonic lavage alters the natural state of mucosal-associated microbiota in the human colon. PLoS One (2012) 1.16
The founding charter of the Genomic Observatories Network. Gigascience (2014) 1.16
Draft genome sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071). J Bacteriol (2012) 1.16
GISMO--gene identification using a support vector machine for ORF classification. Nucleic Acids Res (2006) 1.14
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. Microb Inform Exp (2011) 1.14
From genomics to metagenomics. Curr Opin Biotechnol (2012) 1.13
Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10. Stand Genomic Sci (2010) 1.13
Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9. Stand Genomic Sci (2010) 1.10
Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula. J Biotechnol (2004) 1.06
Connecting genotype to phenotype in the era of high-throughput sequencing. Biochim Biophys Acta (2011) 1.05
Regional differences in colonic mucosa-associated microbiota determine the physiological expression of host heat shock proteins. Am J Physiol Gastrointest Liver Physiol (2010) 1.05
Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol (2010) 1.05
Intestinal tissues induce an SNP mutation in Pseudomonas aeruginosa that enhances its virulence: possible role in anastomotic leak. PLoS One (2012) 1.04
Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses. Phytochemistry (2006) 1.04
Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel. Stand Genomic Sci (2010) 1.01
Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome (2013) 0.96
Combined transcriptome profiling reveals a novel family of arbuscular mycorrhizal-specific Medicago truncatula lectin genes. Mol Plant Microbe Interact (2005) 0.94
A metagenomics portal for a democratized sequencing world. Methods Enzymol (2013) 0.93
Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling. PLoS One (2010) 0.93
Bioinformatics support for high-throughput proteomics. J Biotechnol (2003) 0.92
Maternal activation of gap genes in the hover fly Episyrphus. Development (2010) 0.92
Comprehensive analysis of the extracellular proteins from Xanthomonas campestris pv. campestris B100. Proteomics (2005) 0.92
Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiol Ecol (2008) 0.91
Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010. Stand Genomic Sci (2010) 0.90
Draft genome sequence of Achromobacter piechaudii strain HLE. J Bacteriol (2012) 0.90
The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environ Microbiol (2014) 0.88
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. J Biotechnol (2003) 0.87
Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes. BMC Genomics (2013) 0.86
Mechanisms of age-related decline in memory search across the adult life span. Dev Psychol (2013) 0.86
Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010. Stand Genomic Sci (2010) 0.85
Synergistic use of plant-prokaryote comparative genomics for functional annotations. BMC Genomics (2011) 0.84
Foraging across the life span: is there a reduction in exploration with aging? Front Neurosci (2013) 0.84
Performance benefits of depression: sequential decision making in a healthy sample and a clinically depressed sample. J Abnorm Psychol (2011) 0.84
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. BMC Bioinformatics (2012) 0.84
Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012. Stand Genomic Sci (2012) 0.84
BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae). BMC Genomics (2011) 0.84
Cognitive aging and adaptive foraging behavior. J Gerontol B Psychol Sci Soc Sci (2009) 0.84